Microfabricated "laboratory-on-a-chip" systems are revolutionizing all aspects of genetic analysis. The development of capillary array electrophoresis (CAE) microchannel plate devices makes possible the performance of 96 or more high-speed separations in parallel on a single wafer-scale device. The fluorescently labeled DNA samples are detected within the microchannels with a novel four-color rotary confocal fluorescence scanner. The capabilities of this system for genotyping are demonstrated through multiplex separations of short tandem repeat and hereditary haemochromatosis allele-specific amplicons. Furthermore, with newly developed folded channel designs that maintain high resolution, these CAE microplate systems are used to perform 96 high-quality DNA sequencing separations in parallel to approximately 500 bases per capillary in less than 30 min. These densely packed microfabricated device technologies will facilitate the even more rapid collection of vast amounts of genetic data in the future.